LC-MS/MS Annotation

LC-MS/MS annotation supports unknown compound review, fragmentation matching, and related-family grouping.

Outline

• Upload mzML, mzXML, Waters RAW, or Bruker .d data.
• Review precursor, fragment, and retention-time evidence.
• Compare proposed structures against fragmentation support.
• Group related compounds into LC-MS families.
• Export reviewed evidence into Regentry.

Link to Core Concepts when explaining confidence scores and audit trails.

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Backend capabilities

The MS / structure side of SpectraCheck’s pretrained layer fuses three independent signals into one calibrated candidate ranking; the deterministic structure verifier remains the arbiter of pass/fail. The release timeline gives chronological context.

MS models — CSI:FingerID, METLIN RT & DP4-AI fusion

• CSI:FingerID (MS/MS → structure) — predict_msms_candidates() wraps SIRIUS / CSI:FingerID through its documented interface (env-configured REST service or CLI binary; injectable backend), returning ranked candidate structures + fingerprints. SIRIUS is never reimplemented or bundled, and on a host with no configured backend it degrades gracefully (available=False). (v0.15.0, 2026-06-07)
• METLIN retention-time corroboration — predict_retention_times() + rt_corroboration() apply a Gaussian down-weight on the RT residual, so an RT-inconsistent candidate is demoted, never hard-filtered. (v0.15.0, 2026-06-07)
• DP4-AI posterior + calibrated fusion — dp4_candidate_posterior() reuses the validated in-house DP4 scoring (Smith & Goodman 2010) for a calibrated NMR-candidate posterior, and fuse_candidates() combines NMR (DP4) + MS/MS (CSI) + RT into one ranking summing to 1.0 (RT as a multiplicative down-weight; signal weights renormalise when a signal is missing). Decision-support only — arbitrate() hands the top candidate to the structure verifier. (v0.15.0, 2026-06-07)

Release timeline

Version	Date	Headline
v0.15.0	2026-06-07	MS models: CSI:FingerID, METLIN RT & DP4-AI candidate fusion